Chemdawg ILMN Whole Genome Shotgun data (August 18th 2011)


454- LA Confidential Whole Genome Shotgun data
Jim Knight Assemblies
LA Confidential Chloroplast Sequence
LA Confidential Mitochondrial Sequence
454-LA Confidential Whole Genome Shotgun- SFF

ILMN- LA Confidential- Whole Genome Shotgun data

Low Input Nextera ILMN Whole Genome Shotgun data

Draft WGSequencing was performed on an additional 5 cultivars using Nextera Library preparation techniques and HiSeq 2000 Sequencing. These reads were mapped to the LA confidential assembly under 90% stringency with CLCBio 5.0. SNP calling was performed with CLCBio under default conditions (requiring 5 reads to call a SNP). Due to the low coverage, SNPs are under called.

Each file is broken down into 300MB of reads. They are Paired 100mers with very short inserts. The reads predominantly overlap allowing the paired reads to be extended in a single contiguous read and error corrected.

OG KUSH WGS-READ FILES
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM1_OG_Kush/KJM1/Sample_KJM1/Pair_1/KJM1_TAAGGCGA_L008_R1_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM1_OG_Kush/KJM1/Sample_KJM1/Pair_1/KJM1_TAAGGCGA_L008_R2_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM1_OG_Kush/KJM1/Sample_KJM1/Pair_2/KJM1_TAAGGCGA_L008_R1_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM1_OG_Kush/KJM1/Sample_KJM1/Pair_2/KJM1_TAAGGCGA_L008_R2_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM1_OG_Kush/KJM1/Sample_KJM1/Pair_3/KJM1_TAAGGCGA_L008_R1_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM1_OG_Kush/KJM1/Sample_KJM1/Pair_3/KJM1_TAAGGCGA_L008_R2_003.fastq.gz

CHOCOLOPE SNP FILE
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/KJM2_Chocolope_CGTACTAG_L008_R1_002+(paired)+mapping+SNP+Detection+Table.csv

CHOCOLATE WGS-READ FILES

https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_1/KJM2_CGTACTAG_L008_R1_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_1/KJM2_CGTACTAG_L008_R2_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_2/KJM2_CGTACTAG_L008_R1_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_2/KJM2_CGTACTAG_L008_R2_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_3/KJM2_CGTACTAG_L008_R1_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_3/KJM2_CGTACTAG_L008_R2_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_4/KJM2_CGTACTAG_L008_R1_004.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_4/KJM2_CGTACTAG_L008_R1_004.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_5/KJM2_CGTACTAG_L008_R1_005.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_5/KJM2_CGTACTAG_L008_R2_005.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_6/KJM2_CGTACTAG_L008_R1_006.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM2_Chocolope/Pair_6/KJM2_CGTACTAG_L008_R2_006.fastq.gz

KANDY KUSH SNP FILE
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/KJM3_Kandy_Kush_AGGCAGAA_L008_R1_001+(paired)+mapping+SNP+Detection+Table.csv

KANDY KUSH WGS-READ FILES

https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_1/KJM3_AGGCAGAA_L008_R1_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_1/KJM3_AGGCAGAA_L008_R2_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_2/KJM3_AGGCAGAA_L008_R1_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_2/KJM3_AGGCAGAA_L008_R2_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_3/KJM3_AGGCAGAA_L008_R1_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_3/KJM3_AGGCAGAA_L008_R2_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_4/KJM3_AGGCAGAA_L008_R1_004.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_4/KJM3_AGGCAGAA_L008_R2_004.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_5/KJM3_AGGCAGAA_L008_R1_005.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM3_Kandy_Kush/Sample_KJM3/Pair_5/KJM3_AGGCAGAA_L008_R2_005.fastq.gz

RECON-WGS-READ FILE
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/KJM4_RECON_TCCTGAGC_L008_R1_002+(paired)+mapping+SNP+Detection+Table.csv

https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_1/KJM4_TCCTGAGC_L008_R1_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_1/KJM4_TCCTGAGC_L008_R2_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_2/KJM4_TCCTGAGC_L008_R1_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_2/KJM4_TCCTGAGC_L008_R2_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_3/KJM4_TCCTGAGC_L008_R1_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_3/KJM4_TCCTGAGC_L008_R2_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_4/KJM4_TCCTGAGC_L008_R1_004.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_4/KJM4_TCCTGAGC_L008_R2_004.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_5/KJM4_TCCTGAGC_L008_R1_005.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM4_RECON/Sample_KJM4/Pair_5/KJM4_TCCTGAGC_L008_R2_005.fastq.gz

 

GREEN CRACK WGS-READ FILE
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_1/KJM5_GGACTCCT_L008_R1_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_1/KJM5_GGACTCCT_L008_R2_001.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_2/KJM5_GGACTCCT_L008_R1_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_2/KJM5_GGACTCCT_L008_R2_002.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_3/KJM5_GGACTCCT_L008_R1_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_3/KJM5_GGACTCCT_L008_R2_003.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_4/KJM5_GGACTCCT_L008_R1_004.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_4/KJM5_GGACTCCT_L008_R2_004.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_5/KJM5_GGACTCCT_L008_R1_005.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_5/KJM5_GGACTCCT_L008_R2_005.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_6/KJM5_GGACTCCT_L008_R1_006.fastq.gz

https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_6/KJM5_GGACTCCT_L008_R2_006.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_7/KJM5_GGACTCCT_L008_R1_007.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_7/KJM5_GGACTCCT_L008_R2_007.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_8/KJM5_GGACTCCT_L008_R1_008.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_8/KJM5_GGACTCCT_L008_R2_008.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_9/KJM5_GGACTCCT_L008_R1_009.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_9/KJM5_GGACTCCT_L008_R2_009.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_10/KJM5_GGACTCCT_L008_R1_010.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_10/KJM5_GGACTCCT_L008_R2_010.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_11/KJM5_GGACTCCT_L008_R1_011.fastq.gz
https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/KJM_5_green_CRK/PAIR_1/Pair_11/KJM5_GGACTCCT_L008_R2_011.fastq.gz


2013- In celebration of Colorado and Washington’s move to legalize cannabis we are releasing a 5X draft sequence of another cultivar called Dr. Grinspoon. This technique utilized 20ng of DNA and in theory could be performed non-destructively on a seed such that one could sequence the genome of a seed and then choose to plant or not plant it.

LESTER GRINSPOON-WGS-READ FILE

https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/Dr.+Grinspoon/lane1_KJM_LG_L001_R1_001.fastq.gz

https://s3.amazonaws.com/C.Indica_LA_Confidential/HISEQ_NEXTERA_DATA/Dr.+Grinspoon/lane1_KJM_LG_L001_R2_001.fastq.gz

Thank you to all Jane-Ome subscribers. This work was funded by your curiosity. This is the first decoded genome funded purely through an educational iPad App!


Nla-III RAD-Seq data can be found here

 

 

KannaPedia FastQ

 

 


Oxford Nanopore Whole Genome Shotgun Data

R9.4 MinION-1D B2C2 Whole Genome Shotgun

https://s3.amazonaws.com/nanopore-cannabis/B2C2_34dir.fastq

 

R9.4 MinION 2D other data


Cannabis microbiome ILMN data

There is alot of 16S Cannabis DNA in these studies in addition to 16S and ITS2 Sequence for TAC and TYM testing.

Study 1 & additional samples (a subset of these are in NCBI)

Study II- Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests

 


PacBio THCA synthase data

Single molecule sequencing of THCA synthase reveals copy number variation in modern drug-type Cannabis sativa L.

 


Our Position on Gene Patents:

We do not believe DNA sequences should be the subject matter of patents. Despite this there are over 4700 gene patents filed on the human genome and articles written by Christopher Mason showcase how many human genes are covered by gene patents and how these gene patents are often poorly written and non-specific. Some human gene patents make claims to any 15bp stretch of sequence. These are so non-specific that they include pig and plant genomes. The average gene patent accidentily makes claims to over 690 other human genes simply because the patent office didnt respect the impact of short word sizes in pattern matches. This is the equivalent of a patent claim on the word “The” and by happenstance you also own “their” and “pscyhoTHErapist” and “The I.R.S.”. This table shows how many DNA patents are issued and for which genes (Chris_Mason_Table_S1). Jensen & Murray also highlight this in the below articles.

Pervasive_gene_patents_cover_the_entire_Human_genome

Science-2005-Jensen-239-40

To clarify the scope of patent eligibility in 2013 we designed a method to navigate gene patents. We published this in Nature Biotechnology.

DREAMing of a patent free human genome for clinical sequencing.

The paper caught much attention and remains in the top 5% of articles published.  This paper is behind a paywall so we published the updated methods in the open source journal PLOS-One.

We side with Stephan Kinsella on Intellectual Property being oxymoronic. Property rights cover property. Property must

  • Contain Matter
  • Not be infinitely replicable (exhibit rivalrous scarcity)

Ideas are neither of these.

A reading of these papers will show that there are on average 5 patents per gene. This implies the USPTO is not very effective at prior art searches and our efforts to put the genome public in August of 2011 may not prevent the cannabis genome from becoming the entangled patent thicket we experience on the human genome. For this reason we have filed the below files with the USPTO so they cannot miss them. They are registered with their database and should appear in any preliminary search report. This has created considerable additional expense for us (over $20,000). These patents, once published will be abandoned. Once abandonded they will act as prior art to any future attempts at patenting the cannabis genome and it will leave the vast majority of the cannabis genome Public forever … as it should be!

We understand the Patent system can’t be ignored in biotech entrepreneurship and at times is necessary complication launching companies. These efforts are to dampen overly broad patent claims on simple subject matter like DNA sequences.

A good review on this topic is found at the Property and Freedom Society

https://s3.amazonaws.com/C.Indica_LA_Confidential/SENT_TO_HBSR/Sativa_ChemDawg-Prep7_1-1_1_4.7.2+(paired)+contig+list+(175268+contigs).fa

https://s3.amazonaws.com/C.Indica_LA_Confidential/SENT_TO_HBSR/LA-454-_Assem12_20SFF_0.95_Vote+de+novo+assembly.fa